Published in BMC Genomics on October 11, 2013
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. BMC Genomics (2014) 0.76
Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy. BMC Genomics (2017) 0.75
Evidence of positive selection associated with placental loss in tiger sharks. BMC Evol Biol (2016) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res (2008) 13.51
DNA sequence quality trimming and vector removal. Bioinformatics (2001) 10.04
The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors. Nature (1999) 9.29
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing. Mol Ecol (2008) 9.09
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res (2000) 7.43
Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases. Proc Natl Acad Sci U S A (1994) 6.96
Transoceanic migration, spatial dynamics, and population linkages of white sharks. Science (2005) 5.43
Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet (2005) 5.37
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx. BMC Genomics (2009) 5.14
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Dynamic regulation of pol II transcription by the mammalian Mediator complex. Trends Biochem Sci (2005) 4.37
Biological profiling of gene groups utilizing Gene Ontology. Genome Inform (2005) 4.10
Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science (1994) 3.92
Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. BMC Genomics (2010) 3.84
Construction of a uniform-abundance (normalized) cDNA library. Proc Natl Acad Sci U S A (1991) 3.12
Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol (2007) 2.90
Major reorganization of immunoglobulin VH segmental elements during vertebrate evolution. Nature (1986) 2.46
Instability of short tandem repeats (microsatellites) in human cancers. Nat Genet (1994) 2.45
Global estimates of shark catches using trade records from commercial markets. Ecol Lett (2006) 2.31
TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. Mol Cell (2001) 2.18
Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics (2006) 2.13
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics (2011) 2.02
The complex pathology of trinucleotide repeats. Curr Opin Cell Biol (1997) 1.98
Conserved structures of mediator and RNA polymerase II holoenzyme. Science (1999) 1.97
Microsatellite instability in human solid tumors. Cancer (1998) 1.94
Nephrogenesis is induced by partial nephrectomy in the elasmobranch Leucoraja erinacea. J Am Soc Nephrol (2003) 1.83
A first estimate of white shark, Carcharodon carcharias, abundance off Central California. Biol Lett (2011) 1.65
Role of serine/threonine protein phosphatase 2A in cancer. Cancer Lett (2001) 1.56
Trinucleotide repeat expansions and human genetic disease. Bioessays (1994) 1.55
Ancient noncoding elements conserved in the human genome. Science (2006) 1.53
The mediator of RNA polymerase II. Chromosoma (2005) 1.50
White shark offshore habitat: a behavioral and environmental characterization of the eastern Pacific shared offshore foraging area. PLoS One (2009) 1.48
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. BMC Genomics (2011) 1.45
Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour (2012) 1.44
Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics (2011) 1.43
Regrow or repair: potential regenerative therapies for the kidney. J Am Soc Nephrol (2006) 1.37
A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish. BMC Biol (2009) 1.28
A novel approach for mining polymorphic microsatellite markers in silico. PLoS One (2011) 1.09
Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A (2011) 1.09
Lack of heterogeneity in antihapten antibodies of a phylogenetically primitive shark. Nature (1980) 1.07
Evolution and consequences of endothermy in fishes. Physiol Biochem Zool (2005) 1.06
The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analyses. J Mol Biol (1998) 1.06
When technology meets conservation: increased microsatellite marker production using 454 genome sequencing on the endangered Okaloosa Darter (Etheostoma okaloosae). J Hered (2010) 1.05
Community annotation and bioinformatics workforce development in concert--Little Skate Genome Annotation Workshops and Jamborees. Database (Oxford) (2012) 1.04
Trinucleotide repeat expansions in neurological disease. Curr Opin Neurobiol (1993) 1.03
A role for the polyproline domain of p53 in its regulation by Mdm2. J Biol Chem (2000) 1.01
An ovary transcriptome for all maturational stages of the striped bass (Morone saxatilis), a highly advanced perciform fish. BMC Res Notes (2012) 0.98
Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics (2010) 0.96
Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress. Mol Biol Evol (2002) 0.96
De novo sequence assembly and characterisation of a partial transcriptome for an evolutionarily distinct reptile, the tuatara (Sphenodon punctatus). BMC Genomics (2012) 0.96
A natural deletion of the HoxC cluster in elasmobranch fishes. Science (2011) 0.94
Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances. PLoS One (2010) 0.93
De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques. Mol Ecol Resour (2011) 0.91
The range and fine specificity of the anti-hapten immune response: phylogenetic studies. J Immunogenet (1982) 0.90
Design of heterothermic muscle in fish. J Exp Biol (2002) 0.89
Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu. PLoS One (2011) 0.89
Isolation and characterization of dinucleotide microsatellite loci in the Great White Shark, Carcharodon carcharias. Mol Ecol (2000) 0.87
The multiple shark Ig H chain genes rearrange and hypermutate autonomously. J Immunol (2011) 0.84
Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea). Comp Biochem Physiol Part D Genomics Proteomics (2010) 0.83
Positive selection pressure within teleost Toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafish. Mol Biol Rep (2012) 0.81
Shark cartilage, cancer and the growing threat of pseudoscience. Cancer Res (2004) 0.78
Miiuy croaker hepcidin gene and comparative analyses reveal evidence for positive selection. PLoS One (2012) 0.78
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii). PLoS One (2012) 0.77
Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes. Mol Biol Evol (2002) 3.12
Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol (2007) 3.10
Molecules consolidate the placental mammal tree. Trends Ecol Evol (2004) 3.02
Global estimates of shark catches using trade records from commercial markets. Ecol Lett (2006) 2.31
Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials. Mol Phylogenet Evol (2003) 2.04
Low worldwide genetic diversity in the basking shark (Cetorhinus maximus). Biol Lett (2006) 1.80
Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol Biol Evol (2002) 1.79
Local molecular clocks in three nuclear genes: divergence times for rodents and other mammals and incompatibility among fossil calibrations. J Mol Evol (2003) 1.59
The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol Med Microbiol (2009) 1.59
Molecular evidence for the monophyly of tenrecidae (mammalia) and the timing of the colonization of Madagascar by Malagasy Tenrecs. Mol Phylogenet Evol (2002) 1.56
Virgin birth in a hammerhead shark. Biol Lett (2007) 1.55
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol (2010) 1.54
Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour (2009) 1.43
Novel morphology in Enteromorpha (Ulvophyceae) forming green tides. Am J Bot (2002) 1.41
A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol (2005) 1.34
The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews). Proc Natl Acad Sci U S A (2003) 1.33
Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats. Proc Natl Acad Sci U S A (2002) 1.32
Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol (2012) 1.29
Predominance of genetic monogamy by females in a hammerhead shark, Sphyrna tiburo: implications for shark conservation. Mol Ecol (2004) 1.27
Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect Genet Evol (2011) 1.26
Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals subpopulations of Streptococcus pneumoniae with two distinct methionyl-tRNA synthetase genes. Antimicrob Agents Chemother (2003) 1.21
Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens. EMBO Rep (2003) 1.20
Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phylogenet Evol (2003) 1.16
Identification of shark species composition and proportion in the Hong Kong shark fin market based on molecular genetics and trade records. Conserv Biol (2006) 1.15
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res (2009) 1.15
Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies. Mol Ecol (2007) 1.14
Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol Phylogenet Evol (2002) 1.13
Modelling the spatial dynamics of plasmid transfer and persistence. Microbiology (2007) 1.13
Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol (2011) 1.11
Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes. Mol Phylogenet Evol (2003) 1.06
Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One (2013) 1.05
Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment. J Bacteriol (2014) 1.02
Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts. BMC Genomics (2014) 1.02
Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids. Antonie Van Leeuwenhoek (2009) 1.01
Shark virgin birth produces multiple, viable offspring. J Hered (2010) 1.01
Species delineation and evolutionary history of the globally distributed spotted eagle ray (Aetobatus narinari). J Hered (2009) 0.99
Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol (2014) 0.99
Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLoS One (2013) 0.98
Supplemental feeding for ecotourism reverses diel activity and alters movement patterns and spatial distribution of the southern stingray, Dasyatis americana. PLoS One (2013) 0.98
Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts. Appl Environ Microbiol (2010) 0.96
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC Genomics (2009) 0.95
Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae. PLoS One (2012) 0.95
Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone. Plasmid (2009) 0.94
Comparative characterization of the virulence gene clusters (lipooligosaccharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species. Infect Genet Evol (2012) 0.94
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. BMC Genomics (2012) 0.92
A unique open reading frame within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance. Mol Microbiol (2015) 0.91
Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. J Biochem (2010) 0.88
Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation. Inflamm Bowel Dis (2014) 0.87
The use of composite taxa in supermatrices. Mol Phylogenet Evol (2004) 0.86
Natural selection and mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. Mamm Genome (2006) 0.85
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus. DNA Res (2007) 0.85
Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids. J Bacteriol (2007) 0.85
Replacing and additive horizontal gene transfer in Streptococcus. Mol Biol Evol (2012) 0.85
Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray comparative genomic hybridization. Infect Genet Evol (2008) 0.84
Core-gene-encoded peptide regulating virulence-associated traits in Streptococcus mutans. J Bacteriol (2013) 0.82
Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. Biochem Biophys Res Commun (2005) 0.82
Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.). Genome Announc (2013) 0.81
Low pKa lysine residues at the active site of sarcosine oxidase from Corynebacterium sp. U-96. Biochem Biophys Res Commun (2004) 0.81
Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis. BMC Microbiol (2012) 0.81
Purification, characterization, and molecular cloning of tyrosinase from Pholiota nameko. Biosci Biotechnol Biochem (2007) 0.79
Structural basis of proteolytic activation of L-phenylalanine oxidase from Pseudomonas sp. P-501. J Biol Chem (2008) 0.79
"Lipotyphlan" phylogeny based on the growth hormone receptor gene: a reanalysis. Mol Phylogenet Evol (2004) 0.79
Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum. FEMS Microbiol Lett (2014) 0.78
Surgical treatments for infective endocarditis involving valve annulus. Ann Thorac Cardiovasc Surg (2009) 0.78
The behavioural and genetic mating system of the sand tiger shark, Carcharias taurus, an intrauterine cannibal. Biol Lett (2013) 0.78
A streamlined DNA tool for global identification of heavily exploited coastal shark species (genus Rhizoprionodon). PLoS One (2012) 0.77
High resolution X-ray crystal structures of L-phenylalanine oxidase (deaminating and decarboxylating) from Pseudomonas sp. P-501. Structures of the enzyme-ligand complex and catalytic mechanism. J Biochem (2011) 0.76
Site-directed mutagenesis study of the antibody 2D7 which catalyzes a reaction for insertion of Cu2+ into mesoporphyrin. J Biosci Bioeng (2005) 0.76
A comprehensive software suite for the analysis of cDNAs. Genomics Proteomics Bioinformatics (2005) 0.75
Functional bias of positively selected genes in Streptococcus genomes. Infect Genet Evol (2011) 0.75
Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum. Genome Announc (2013) 0.75
Methods for data mining from large multinational surveillance studies. Antimicrob Agents Chemother (2002) 0.75
Papillary muscle head approximation for the treatment of mitral valve regurgitation combined with aortic valve disease. Int Heart J (2010) 0.75
Combined surgery for ischemic cardiomyopathy: report of a case. J Cardiol (2008) 0.75
Deuterium kinetic isotope effects in heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96: the anionic form of the substrate in the enzyme-substrate complex is a reactive species. J Biochem (2012) 0.75
RbcL sequences indicate a single evolutionary origin of multinucleate cells in the red algal tribe Callithamnieae. Mol Phylogenet Evol (2002) 0.75
Kinetic isotope effect of the L-phenylalanine oxidase from Pseudomonas sp. P-501. J Biochem (2006) 0.75
Original papillary muscle sandwich plasty for ischemic mitral regurgitation. Circ J (2009) 0.75
Papillary muscle sandwich plasty for ischemic mitral regurgitation: a new simple technique. J Thorac Cardiovasc Surg (2008) 0.75
Cofactors in sarcosine oxidase from Corynebacterium sp. U-96. J Protein Chem (2002) 0.75
Characterization of putative tryptophan monooxygenase from Ralstonia solanacearum [corrected]. J Biochem (2009) 0.75
Kinetic studies on the role of Lys-171 and Lys-358 in the beta subunit of sarcosine oxidase from Corynebacterium sp. U-96. J Biochem (2007) 0.75